Commits · a54ff3e8f67ca30cfe1e055360828a0f02446848 · zavolan_group / pipelines / ZARP · GitLab

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Mar 06, 2020
- Generate bedgraph file of normalised coverage. Fixes #45 · a54ff3e8
  Dominik Burri authored 5 years ago and BIOPZ-Gypas Foivos committed 5 years ago
  
  a54ff3e8
- Extract transcript sequences from genome (fasta file) and gene annotations (gtf file). Fixes #62 · 7784fc9b
  BIOPZ-Gypas Foivos authored 5 years ago
  
  7784fc9b
- Extract transcript sequences from genome (fasta file) and gene annotations (gtf file). Fixes #62 · 0def7b72
  BIOPZ-Iborra de Toledo Paula authored 5 years ago and BIOPZ-Gypas Foivos committed 5 years ago
  
  0def7b72
- Closes #76 and #79 · 88e3914b
  BIOPZ-Gypas Foivos authored 5 years ago
  
  88e3914b
- Separate stdout and stderr logs for the majority of rules. Closes #76 and #79 · ff0a39fa
  BIOPZ-Katsantoni Maria authored 5 years ago and BIOPZ-Gypas Foivos committed 5 years ago
  
  ff0a39fa
Feb 24, 2020
- Merge branch 'generate_gene_count_tables_from_salmon' into 'master' · f31261b5
  Alex Kanitz authored 5 years ago
  f31261b5
- Add rule that combines counts from Salmon · 357ed828
  BIOPZ-Gypas Foivos authored 5 years ago and Alex Kanitz committed 5 years ago
  357ed828
Feb 21, 2020
- Merge branch 'use_minified_docker_images' into 'master' · 0c039203
  Alex Kanitz authored 5 years ago
  0c039203
- Use minified docker images · dc2afcf9
  Alex Kanitz authored 5 years ago
  
  dc2afcf9
- Merge branch 'generate_gene_count_tables' into 'master' · 13975de8
  Alex Kanitz authored 5 years ago
  13975de8
- Add rule that combines TPM values from Salmon · bb1f9b8f
  BIOPZ-Iborra de Toledo Paula authored 5 years ago and Alex Kanitz committed 5 years ago
  bb1f9b8f
- Merge branch 'input_features' into 'master' · 641f2cbb
  Alex Kanitz authored 5 years ago
  641f2cbb
- handle polyA processing in input preparation script · c4e20a21
  BIOPZ-Katsantoni Maria authored 5 years ago and Alex Kanitz committed 5 years ago
  c4e20a21
Feb 20, 2020
- Merge branch 'log_dirs' into 'master' · c58f28df
  Alex Kanitz authored 5 years ago
  c58f28df
- create log directories in Snakefile\ · 5e1ec85e
  Alex Kanitz authored 5 years ago
  5e1ec85e
Feb 18, 2020
- Merge branch 'hotfix_docs_missing_link' into 'master' · 1f933bcc
  Alex Kanitz authored 5 years ago
  1f933bcc
- fix broken links in docs · 1782ea86
  Alex Kanitz authored 5 years ago
  
  1782ea86
- Merge branch 'conda_env' into 'master' · 885c5692
  Alex Kanitz authored 5 years ago
  885c5692
- install dependencies via Conda · 8742cd72
  Alex Kanitz authored 5 years ago
  8742cd72
- Merge branch 'verbose_tests' into 'master' · 4ad34d82
  Alex Kanitz authored 5 years ago
  4ad34d82
- run tests in verbose mode · 0d95577e
  Alex Kanitz authored 5 years ago
  0d95577e
Feb 17, 2020
- Merge branch 'TIN' into 'master' · ba39b976
  Alex Kanitz authored 5 years ago
  ba39b976
- add TIN score calculation · c538fe8b
  BIOPZ-Bak Maciej authored 5 years ago and Alex Kanitz committed 5 years ago
  c538fe8b
Feb 15, 2020
- Merge branch 'labkey_api_input_parser' into 'master' · a654943c
  Alex Kanitz authored 5 years ago
  a654943c
- get Snakemake input from LabKey API · eea0206f
  BIOPZ-Katsantoni Maria authored 5 years ago and Alex Kanitz committed 5 years ago
  eea0206f
Feb 14, 2020
- Merge branch 'recommended_repo_structure' into 'master' · fdc358f4
  Alex Kanitz authored 5 years ago
  fdc358f4
- repo follows recommended structure · 1e52fa56
  Alex Kanitz authored 5 years ago
  
  1e52fa56
- Merge branch 'hotfix_integration_test' into 'master' · 39b7ea7b
  Alex Kanitz authored 5 years ago
  39b7ea7b
- hot fix integration test script · 3fe8f0d1
  Alex Kanitz authored 5 years ago
  
  3fe8f0d1
- Merge branch 'merge_api_input_parse' into 'master' · e7ac9662
  Alex Kanitz authored 5 years ago
  e7ac9662
- LabKey-like input to Snakmake input · 979e6cdd
  BIOPZ-Katsantoni Maria authored 5 years ago and Alex Kanitz committed 5 years ago
  979e6cdd
- Merge branch 'check_readme' into 'master' · c5c4a29e
  Alex Kanitz authored 5 years ago
  c5c4a29e
- update install instructions · 60597a61
  CJHerrmann authored 5 years ago and Alex Kanitz committed 5 years ago
  60597a61
- Merge branch '52-display-rulegraph-instead-of-dag' into 'master' · dbc37e38
  Alex Kanitz authored 5 years ago
  dbc37e38
- display rule graph instead of DAG · ff08b9c3
  CJHerrmann authored 5 years ago and Alex Kanitz committed 5 years ago
  ff08b9c3
- Merge branch 'ground_truth_checks' into 'master' · 7c93122f
  Alex Kanitz authored 5 years ago
  7c93122f
- verify test workflow output against ground truth · c6341db2
  Alex Kanitz authored 5 years ago
  c6341db2
Feb 09, 2020
- Merge branch 'test_files' into 'master' · 7f243c20
  Alex Kanitz authored 5 years ago
  7f243c20
- replace test files with small synthetic ones · 48e012a0
  Alex Kanitz authored 5 years ago
  48e012a0
Feb 08, 2020
- Merge branch 'subpipelines' into 'master' · d60fefdc
  Alex Kanitz authored 5 years ago
  d60fefdc